CD-DVD/DiscSpeed's quality score is based on PIF (and POF, for the BenQ) alone. If there are no POF (or POF aren't reported), it is strictly dependent on PIF, given that is the worst digital error type being reported. (Should another drive be used that reports only POE or PIE, the QS will depend on that, but that doesn't apply in many/any cases around here).
You'll notice that the BenQ and Optiarc scans get the same score, because they report the same PIF max (PIF = 6) and use the same sampling interval (8 ECC). The Samsung and LiteOn each use a different scanning interval (1 ECC), and report a different max PIF (PIF = 3).
With the change in scanning interval comes a change in QS calculation. Hence the difference. The PIF max of 6 looks worse, but for those drives, it's actually treated as being better.
Jitter is not taken into account; however, you eventually get a feel for what is good and what isn't good relative to your drive/firmware/media/speed combination.
[note: I am not good with words this early in the morning, so the above is likely inaccurate, but a good enough start].
I advise you to re-read and re-process as many of the scanning articles located on the site. Though the software might have changed, the information is still relevant as far as CD & DVD scanning goes.
As far as the advanced scanning goes...yes, it might get a class 3 due to PIE, but the attention isn't squarely placed on the "class" rating when one does an advanced disc quality scan. It's more helpful to see how severe each type of error really is over the span of the disc. [That's not to say the class rating is useless; you just have to see what causes it and determine if it's a big concern whatsoever.]